MySQL COUNT DISTINCT

 Select
     Count(Distinct user_id) As countUsers
   , Count(site_id) As countVisits
   , site_id As site
 From cp_visits
 Where ts >= DATE_SUB(NOW(), INTERVAL 1 DAY)
 Group By site_id

Overall

SELECT
       COUNT(DISTINCT `site_id`) as distinct_sites
  FROM `cp_visits`
 WHERE ts >= DATE_SUB(NOW(), INTERVAL 1 DAY)

Or per site

  SELECT
         `site_id` as site,
         COUNT(DISTINCT `user_id`) as distinct_users_per_site
    FROM `cp_visits`
   WHERE ts >= DATE_SUB(NOW(), INTERVAL 1 DAY)
GROUP BY `site_id`

Having the time column in the result doesn't make sense - since you are aggregating the rows, showing one particular time is irrelevant, unless it is the min or max you are after.

You need to use a group by clause.

SELECT  site_id, MAX(ts) as TIME, count(*) group by site_id